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 > Important Notice Regarding Tannerella forsythia (strain 92A2)
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 >HOMD 16S rRNA Reference Sequence Version 11.0 has been released
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 >Publication: Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples
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Important Notice Regarding Tannerella forsythia (strain 92A2)
Dear Research Community:

I wish to call to your attention an error in the strain attribution for the Tannerella forsythia (previously Bacteroides forsythus) genome sequence NC_016610.1. More than 10 years ago, DNA was prepared at Forsyth by Mark Maiden from strain 92A2 and sent to TIGR for sequencing as part of the initial 11 dental organisms sequenced. The sequence was obtained by TIGR, annotated by Los Alamos, and posted on Los Alamos and Forsyth web sites in about 2005. JCVI re-annotated the genome in 2013 as part of the HMP project and released the genome through NCBI in July 2013. Unfortunately, at some point in time, someone assumed that Forsyth strain 92A2 was the same as the Tannerella forsythia (previously Bacteroides forsythus) type strain FDC-338 = ATCC 43037. It is not. More problematic, strain 92A2 was never deposited with ATCC(we are in the process of doing that currently). In the move from Boston to Cambridge in 2010, Forsyth investigators discarded many old stocks, sadly including 92A2. After many inquiries, I was extremely relieved to find that Gene Leys and Christina Igboin had frozen stocks at Ohio State University. With their help, we now have Tannerella forsythia strain 92A2 growing and save away here at Forsyth again. The strain was chosen for sequencing because it contains a tetracycline transposon which was of interest. Most Tannerella forsythia strains do not have this transposon. I have validated our current 92A2 strain as the TIGR-sequenced strain by obtaining the 16S rRNA sequence, and by sequencing the TraG gene from the Transposon. Both are perfect matches.

A true genome sequence for the type strain (ATCC 43037) has been obtained by Valentin Friedrich, BOKU, Vienna, Austria. I hope to have this annotated genome available on HOMD shortly and also deposit it with NCBI. I have also contacted Karen Nelson at JCVI to assist in correcting the strain attribution at NCBI for the TIGR/92A2 genome (only the depositor can make changes).

This strain misattribution has cause significant wasted effort by investigators trying to clone out genes or perform other molecular biology. I apologize to the community for not realizing 92A2 had not been deposited with a culture collection and not picking up the strain attribution problem earlier. The attribution was correct 2005 when Tsute (George) Chen referenced the strain in the following publication and on the BROP website:

Chen T, Abbey K, Deng WJ, Cheng MC. The bioinformatics resource for oral pathogens. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W734-40. PubMed PMID: 15980574; PubMed Central PMCID: PMC1160122.

It may take some time for strain 92A2 to become available from ATCC. If you urgently need this strain for ongoing studies, please contact me and I will send it to you. If you can wait until ATCC has it available, that would be most helpful to my technicians. Please do not pester Gene for the strain, or Valentin for the type genome as they have performed their community service already and Im willing to be the resource contact person. The Tannerella forsythia entry on HOMD has a warning flag about the strain attribution problem, and a correction on the strain Sequence Meta Information page, but I cannot edit the incorrect strain information automatically downloaded from NCBI. As additional information becomes available, I will post it on HOMD Tannerella forsythia taxon description page. Feel free to contact me.

Best regards,

Floyd

Floyd E. Dewhirst, DDS, PhD
Department of Microbiology
The Forsyth Institute
245 First Street
Cambridge, MA 02142


Article last modified on 2014-10-07 15:02:46 by tsute; viewed 1611 times; Category: General Documentation; Topic: Announcement

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